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Re: Princeton Field Guide



"Phylogenetic nomenclature, on the other hand, assumes evolution and uses 
tree-thinking; this makes everything easier."

Problem is, it assumes (or at least works most conveniently with) a 
branching-tree model of evolution (cladogenesis); it has issues with anagenesis 
and reticulate evolution.

This is why I suggest that there should be 'one remove' between the clade as a 
biological entity and the taxonomic unit; even if they contain the same 
organisms (as they *usually* should) the mental distinction is important to 
retain -- one's a biological entity, one's a tool for talking about biological 
diversity.

William Miller
----- Original Message -----
From: "David Marjanovic" <david.marjanovic@gmx.at>
To: "DML" <dinosaur@usc.edu>
Sent: Thursday, October 21, 2010 12:03:22 PM GMT -06:00 US/Canada Central
Subject: Re: Princeton Field Guide

  > I have 1) a general statement on the matter, and 2) a direct reply
>  to one of Greg's arguments.
>
>  1)
>
>  I mostly agree with Jaime here, although I differ slightly in
>  interpretation. I think that "species" can be defined so as to make
>  it a term describing real entities (phylogenetic species concept,
>  i.e. distinct evolutionary destinies), but I would also say that
>  there are, practical sense, so many hurdles to actually identifying
>  and measuring species as distinct entities - and to applying any
>  single species concept across all of biology, without special
>  pleading for umpteen different subfields - that the concept of
>  "species" in any hard-and-fast sense is useless. It is good only as
>  an approximation to ease communication somewhat.

I think the real problem is Linnaean nomenclature, which requires us to 
shoehorn every organism into a species (and a genus) if we are to put it 
into any kind of system at all.

If we ignore this requirement, and the PhyloCode will let us, everything 
suddenly looks a lot different. For instance, "phylogenetic species" 
turns out to be just a synonym of LITU (Least Inclusive Taxonomic Unit = 
smallest recognizable clade; a term not used by the PhyloCode, but fully 
compatible with it). Why use the separate term "species" for it? There 
is no reason.

Other species concepts, too, describe real entities. If you're 
interested in gene flow between populations, the good old Biological 
Species Concepts (both of them*) describe useful entities (ring species 
included), laborious as they are to discover; they're just often not 
congruent with ecological species, morphological species, or 
phylogenetic species. All these concepts have nothing in common except 
the _word_ "species". _There is no_ Platonic ideal of "species" that 
these concepts approach, as so many people still seem to think.

* _Can_ they produce fertile offspring in captivity vs. _do_ they do so 
in the wild.

>  I believe "species" can be addressed logically, as stated, but not
>  observed and measured adequately. That still gives us some basis for
>  saying it is a real concept. "Genus," however, has never been
>  measured, nor to my knowledge has it ever been given any definition
>  that can validate its existence through logic alone.

There is a definition of "genus". It's an extrapolation of the 
Biological Species Concepts: if they (can) have fertile offspring, 
they're in the same species; if they (can) have sterile offspring, 
they're different species in the same genus; if they can't have 
offspring at all, they're in different genera.

Unsurprisingly, almost nobody has ever tried to use this definition. 
Like the BSC, it's impossible to use for anything but extant sexually 
reproducing organisms, and very difficult in practice to apply even to 
those; like the BSC, it would trigger a lot of lumping, in some cases to 
the point that several traditional subfamilies would have to be merged 
into a single genus; and in addition to ring species, we'd get sphere 
genera.

>  The concept is somewhat useful as a sort of "handle" by which we can
>  mentally "pick up" various similar species-ish taxa simultaneously -
>  a sort of shorthand, really - but that's about it. It lets us
>  conceptually grab bunches of species together instead of listing the
>  whole lot or constantly laying out the definition of their clade.

The _name_ of the clade in question does this, not the _rank_ of genus 
(or any other rank).

>  Genera are therefore subjective. If we agree on their content by
>  convention, then so be it, because we know what we mean by it and it
>  hypothetically facilitates communication.

Problem is, there is no consensus, and the ICZN doesn't even try to help:

> >Principles

There are certain underlying principles upon which the Code is based. 
These are as follows:

(1) The Code refrains from infringing upon taxonomic judgment, which 
must not be made subject to regulation or restraint.

(2) Nomenclature does not determine the inclusiveness or exclusiveness 
of any taxon, nor the rank to be accorded to any assemblage of animals, 
but, rather, provides the name that is to be used for a taxon whatever 
taxonomic limits and rank are given to it.<<

http://www.nhm.ac.uk/hosted-sites/iczn/code/includes/page.jsp?nfv=&booksection=introduction

Anyone can publish a classification that assigns however many species to 
any genus as they damn well please. And then anyone else can come along 
and publish a classification that contradicts it. And to all eternity 
both are correct, and neither is wrong, provided they keep the type 
species in their genera and obey priority.

(...Never mind that the mandatory suffixes for family-group ranks and 
the mandatory formats for genus-group and species-group names contradict 
Principle 2 rather blatantly.)

So, if I say "*Bufo*", do I mean the mid-20th-century *Bufo* which 
includes all hundreds of bufonids that aren't too weird, or the much, 
much smaller Frost et al. (2006) concept of *Bufo* which is limited to a 
couple of Eurasian species, so that the cane toad is *Rhinella marina*? 
The name alone doesn't tell you, and neither does the (unchanged) genus 
rank of that name.

>  If we start talking about inclusion or exclusion of taxa according to
>  phylogeny as elucidated by traits, we're applying objective reasoning
>  to a subjective construct. That does not work. Only subjective
>  consensus applies to defining subjective phenomena. So saying that we
>  should or shouldn't include taxa in a genus based "only" on traits
>  like frill horns or whatnot is absurd, because we can subjectively
>  attach as much or as little significance to any given trait as we
>  collectively agree to do.

We don't even need to agree. It's enough that the ICZN lets us.

>  Greg's subjective preference that we give less value to such
>  features is not wrong by any means, it's just not the standard agreed
>  upon by a larger set of people-interested-in-the-issue.

There isn't a standard in the first place.

>  Greg's standard has therefore been excluded by subjective consensus;

That consensus consists only of which species to include in which genera 
of Mesozoic dinosaurs. There's not much, if any, of a general concept 
behind it.

>  2)
>
>  Some point-by-point responses to a particular line of reasoning:
>
>  "It is not possible to define species either, but species are real."
>
>  As far as science is concerned. all real things have a definition.

Really?

>  "It is not possible to define life, but it is real."
>
>  "Life" is a loaded word. I would argue that reasonable definitions
>  for it do exist, as long as we're careful about "unloading" it first
>  to avoid confusion.

It's a continuum that our languages fail to express. Therefore, where in 
the continuum we decide to draw the line is completely subjective. Are 
viruses living beings? Depends on how we choose to define "life". :-| If 
we want viruses to count as "alive", we'll likely define "life" along 
criteria of information; if we don't want them to count, we'll likely 
use things like independent metabolism as defining. It's up to us.

>  "There is no way to precisely define battleship versus battlecruiser
>  (HMS HOOD for example) versus heavy cruiser (Alaska class for
>  example)."
>
>  That's because, philosophically, there's no such thing as a
>  "battleship," "battlecruiser, or "cruiser." Let me clarify. The
>  designs for those vessels exist; the vessels themselves exist as
>  physical objects. They are real and they are mathematically
>  definable. But the categorizations for them are ultimately arbitrary
>  human labels. Yes, one could say "semi-arbitrary," because tonnage
>  and certain other factors are measurable as portions of a continuum,
>  which is what such terms are attempting to encapsulate. Yet, like
>  language in general, the labels themselves have no fixed meaning, and
>  further, there are so many continua being lumped together (tonnage,
>  dimensions, # of guns, etc) that a huge number of variations along
>  one or all continua are possible. We could define every possible
>  combination along every last axis if we had the time and inclination
>  to do so, but it's such a complex question that no one has the
>  wherewithal to attempt it, and that would still leave us with a
>  radically different form of classification.
>
>  In point of fact, there is no *empirical* dividing line along any
>  continuum at which one category turns into another, except in our
>  own minds due our own subjective preferences (because in this case
>  we *want* categories, so we delineate them at our convenience. We
>  could choose to lump them all into a single category if we desired to
>  do so, or we could break them down until we only talk about specific
>  designs, specific mission profiles, or specific vessels). The
>  physical world only shows that one ship has X guns and another ship
>  has Y, *not* that this difference has significance in any absolute
>  sense, and therefore *not* that this difference demands any
>  *specific* nomenclature for categorization. The only significance is
>  in our minds, and hence the terms we apply to individual designs are
>  still arbitrary designations - except insofar as we wish to
>  communicate useful information (so while we could call a
>  "battlecruiser" a "flying spaghetti warship" if we so wished, we
>  prefer to use the term that will convey meaning more effectively to
>  those who might otherwise be confused).

You are, thus, saying that, "philosophically, there's no such thing as" 
life.

I'm fine with that.

>  "Many terms are approximations, it does not mean that they cannot be
>  used to describe and distinguish basic, comparable types."
>
>  Right. Approximations. General notions. Not things we can be
>  definite about. So not, for example, things we can definitely say
>  include or exclude any one taxon.

Phylogenetic nomenclature escapes this by using objectively discoverable 
events to define clade names. Rank-based nomenclature doesn't even try.

That's because rank-based nomenclature is deliberately theory-free. Both 
Charles Darwin and Richard Owen, together with many others, are among 
the authors of the 1842/3 Strickland code of zoological nomenclature, so 
it's a worst-of-all-worlds compromise. It treats organisms as 
battleships, battle cruisers and heavy cruisers. Phylogenetic 
nomenclature, on the other hand, assumes evolution and uses 
tree-thinking; this makes everything easier.